Starting phenix.real_space_refine on Tue Mar 19 07:09:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlk_14783/03_2024/7zlk_14783.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 14758 2.51 5 N 3941 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23518 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 954 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "Q" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "T" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.05, per 1000 atoms: 0.51 Number of scatterers: 23518 At special positions: 0 Unit cell: (151.8, 151.8, 170.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4678 8.00 N 3941 7.00 C 14758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.19 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.02 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 86 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 7 " " MAN J 4 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 7 " " MAN c 4 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " " BMA K 3 " - " MAN K 4 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 188 " " NAG A 605 " - " ASN A 362 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 188 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 88 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 241 " " NAG D 604 " - " ASN D 289 " " NAG D 605 " - " ASN D 189 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 386 " " NAG D 608 " - " ASN D 88 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 448 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 301 " Time building additional restraints: 10.32 Conformation dependent library (CDL) restraints added in 3.1 seconds 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 19.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.044A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.053A pdb=" N ARG A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.995A pdb=" N GLN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 545 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 569 through 596 removed outlier: 5.482A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 631 through 649 removed outlier: 4.014A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.566A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.293A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 535 Processing helix chain 'E' and resid 536 through 545 removed outlier: 3.614A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.611A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.889A pdb=" N LYS D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.516A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 543 through 550 removed outlier: 3.879A pdb=" N VAL F 549 " --> pdb=" O LEU F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 556 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 652 through 662 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.599A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.648A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 77 through 81 Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.503A pdb=" N HIS S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 5.733A pdb=" N SER S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.298A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.917A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.860A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.170A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 310 removed outlier: 6.929A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.760A pdb=" N ARG C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.350A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.876A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 416 Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 310 removed outlier: 6.724A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.251A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.801A pdb=" N ARG D 66 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.714A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.614A pdb=" N HIS D 374 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.762A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.951A pdb=" N TYR M 33 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.078A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 8 through 11 removed outlier: 6.559A pdb=" N TRP N 33 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AE3, first strand: chain 'N' and resid 17 through 22 Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 8 Processing sheet with id=AE5, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.948A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.755A pdb=" N TRP Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.581A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'S' and resid 57 through 59 removed outlier: 6.677A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR S 33 " --> pdb=" O GLU S 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.606A pdb=" N TRP T 33 " --> pdb=" O VAL T 45 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 8 through 11 Processing sheet with id=AF9, first strand: chain 'T' and resid 17 through 22 889 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 11.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4525 1.32 - 1.46: 8381 1.46 - 1.60: 10899 1.60 - 1.75: 41 1.75 - 1.89: 181 Bond restraints: 24027 Sorted by residual: bond pdb=" N PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" CB HIS D 308 " pdb=" CG HIS D 308 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.29e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" CB LEU T 107 " pdb=" CG LEU T 107 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PHE Q 29 " pdb=" CG PHE Q 29 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 ... (remaining 24022 not shown) Histogram of bond angle deviations from ideal: 95.02 - 104.08: 398 104.08 - 113.14: 13117 113.14 - 122.20: 14657 122.20 - 131.26: 4383 131.26 - 140.32: 113 Bond angle restraints: 32668 Sorted by residual: angle pdb=" N ASP S 101 " pdb=" CA ASP S 101 " pdb=" C ASP S 101 " ideal model delta sigma weight residual 109.81 140.32 -30.51 2.21e+00 2.05e-01 1.91e+02 angle pdb=" N PHE Q 29 " pdb=" CA PHE Q 29 " pdb=" C PHE Q 29 " ideal model delta sigma weight residual 113.02 127.64 -14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" N PHE H 29 " pdb=" CA PHE H 29 " pdb=" C PHE H 29 " ideal model delta sigma weight residual 113.02 126.23 -13.21 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N THR P 92 " pdb=" CA THR P 92 " pdb=" C THR P 92 " ideal model delta sigma weight residual 111.36 122.50 -11.14 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N PRO S 102 " pdb=" CA PRO S 102 " pdb=" C PRO S 102 " ideal model delta sigma weight residual 113.40 100.56 12.84 1.34e+00 5.57e-01 9.18e+01 ... (remaining 32663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 14997 21.69 - 43.38: 361 43.38 - 65.07: 100 65.07 - 86.76: 108 86.76 - 108.45: 57 Dihedral angle restraints: 15623 sinusoidal: 7453 harmonic: 8170 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -164.40 78.40 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -163.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -140.56 54.56 1 1.00e+01 1.00e-02 4.03e+01 ... (remaining 15620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3091 0.141 - 0.283: 659 0.283 - 0.424: 152 0.424 - 0.565: 42 0.565 - 0.707: 2 Chirality restraints: 3946 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 3943 not shown) Planarity restraints: 4037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.314 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG b 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 608 " 0.254 2.00e-02 2.50e+03 2.10e-01 5.53e+02 pdb=" C7 NAG D 608 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG D 608 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 608 " -0.347 2.00e-02 2.50e+03 pdb=" O7 NAG D 608 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 603 " 0.225 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG D 603 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 603 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG D 603 " -0.315 2.00e-02 2.50e+03 pdb=" O7 NAG D 603 " 0.176 2.00e-02 2.50e+03 ... (remaining 4034 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7414 2.86 - 3.37: 21544 3.37 - 3.88: 39653 3.88 - 4.39: 45561 4.39 - 4.90: 72660 Nonbonded interactions: 186832 Sorted by model distance: nonbonded pdb=" O PHE S 100H" pdb=" NE1 TRP S 103 " model vdw 2.348 2.520 nonbonded pdb=" N ALA F 541 " pdb=" O ALA F 541 " model vdw 2.357 2.496 nonbonded pdb=" N ALA B 533 " pdb=" N SER B 534 " model vdw 2.375 2.560 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 429 " model vdw 2.380 2.520 nonbonded pdb=" NZ LYS D 500 " pdb=" OD2 ASP N 51 " model vdw 2.394 2.520 ... (remaining 186827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 35 through 502 or resid 601 through 605)) selection = (chain 'D' and (resid 35 through 502 or resid 601 through 605)) } ncs_group { reference = (chain 'B' and (resid 523 through 558 or resid 569 through 651)) selection = (chain 'E' and resid 523 through 651) selection = (chain 'F' and resid 523 through 651) } ncs_group { reference = chain 'G' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 7)) selection = (chain 'X' and (resid 1 or resid 4 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 7)) selection = (chain 'd' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'M' and resid 1 through 108) selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.430 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 60.580 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.142 24027 Z= 1.390 Angle : 1.849 30.506 32668 Z= 1.216 Chirality : 0.131 0.707 3946 Planarity : 0.011 0.273 4000 Dihedral : 14.463 108.451 10232 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2780 helix: -0.23 (0.23), residues: 387 sheet: 0.75 (0.16), residues: 844 loop : 0.16 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.011 TRP O 47 HIS 0.009 0.002 HIS C 374 PHE 0.050 0.007 PHE M 52 TYR 0.062 0.009 TYR T 48 ARG 0.009 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 872 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8654 (t) cc_final: 0.8396 (p) REVERT: A 78 ASP cc_start: 0.8379 (m-30) cc_final: 0.7796 (t70) REVERT: A 95 MET cc_start: 0.8766 (ptt) cc_final: 0.8552 (ppp) REVERT: A 180 ASP cc_start: 0.8380 (m-30) cc_final: 0.8164 (m-30) REVERT: A 284 ILE cc_start: 0.8443 (mt) cc_final: 0.8050 (tt) REVERT: A 368 ASP cc_start: 0.8253 (t0) cc_final: 0.7972 (t0) REVERT: A 387 THR cc_start: 0.8315 (p) cc_final: 0.8029 (t) REVERT: A 391 PHE cc_start: 0.8865 (m-80) cc_final: 0.8665 (m-10) REVERT: A 426 MET cc_start: 0.6826 (mtp) cc_final: 0.6424 (mtm) REVERT: B 523 LEU cc_start: 0.8850 (mt) cc_final: 0.8547 (mt) REVERT: B 530 MET cc_start: 0.3290 (mmp) cc_final: 0.2913 (mmp) REVERT: B 624 ASN cc_start: 0.6565 (m-40) cc_final: 0.5289 (t0) REVERT: B 631 TRP cc_start: 0.6428 (m-10) cc_final: 0.6179 (m-10) REVERT: C 42 VAL cc_start: 0.9391 (t) cc_final: 0.9185 (p) REVERT: C 68 VAL cc_start: 0.9051 (p) cc_final: 0.8726 (p) REVERT: C 103 GLN cc_start: 0.8420 (tp40) cc_final: 0.7815 (tm-30) REVERT: C 165 ILE cc_start: 0.8293 (mt) cc_final: 0.8031 (mm) REVERT: C 370 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7838 (mp0) REVERT: C 419 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7876 (mtp180) REVERT: E 530 MET cc_start: 0.8201 (mtp) cc_final: 0.7736 (mtm) REVERT: E 601 LYS cc_start: 0.8310 (mttt) cc_final: 0.7629 (mtmt) REVERT: E 618 SER cc_start: 0.8218 (m) cc_final: 0.7981 (p) REVERT: E 638 TYR cc_start: 0.8011 (m-80) cc_final: 0.7635 (m-80) REVERT: E 639 THR cc_start: 0.8432 (m) cc_final: 0.7565 (t) REVERT: E 644 ASN cc_start: 0.8449 (m-40) cc_final: 0.8181 (t0) REVERT: E 648 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 92 ASN cc_start: 0.7693 (t0) cc_final: 0.7459 (t0) REVERT: D 198 THR cc_start: 0.8509 (m) cc_final: 0.8252 (p) REVERT: D 246 GLN cc_start: 0.7241 (mp10) cc_final: 0.5893 (tp40) REVERT: D 373 MET cc_start: 0.7682 (mtm) cc_final: 0.6953 (mtp) REVERT: D 434 MET cc_start: 0.8221 (ttm) cc_final: 0.7980 (ttp) REVERT: D 468 PHE cc_start: 0.7609 (m-80) cc_final: 0.6947 (m-80) REVERT: F 540 GLN cc_start: 0.8985 (tp40) cc_final: 0.8493 (tp40) REVERT: F 545 LEU cc_start: 0.9008 (tp) cc_final: 0.8498 (tt) REVERT: F 601 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8718 (mmtp) REVERT: F 623 TRP cc_start: 0.9149 (m100) cc_final: 0.8679 (m100) REVERT: H 81 LYS cc_start: 0.8180 (tttt) cc_final: 0.7919 (mmtm) REVERT: H 82 MET cc_start: 0.6850 (tpp) cc_final: 0.6322 (tpp) REVERT: H 93 VAL cc_start: 0.8808 (t) cc_final: 0.8212 (m) REVERT: H 110 LEU cc_start: 0.8435 (tp) cc_final: 0.8228 (tp) REVERT: L 27 GLN cc_start: 0.7333 (tp-100) cc_final: 0.7045 (tm-30) REVERT: L 27 LEU cc_start: 0.8126 (mt) cc_final: 0.7794 (mt) REVERT: L 60 ASP cc_start: 0.8466 (p0) cc_final: 0.8173 (p0) REVERT: L 61 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8008 (mtm-85) REVERT: L 97 THR cc_start: 0.8924 (t) cc_final: 0.8688 (t) REVERT: M 72 ASP cc_start: 0.7924 (t0) cc_final: 0.7422 (t0) REVERT: M 86 ASP cc_start: 0.8216 (m-30) cc_final: 0.7948 (m-30) REVERT: M 91 TYR cc_start: 0.7775 (m-80) cc_final: 0.7540 (m-80) REVERT: M 100 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8372 (tt0) REVERT: N 49 ASP cc_start: 0.8065 (m-30) cc_final: 0.7794 (m-30) REVERT: N 52 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7207 (mtp-110) REVERT: N 60 PHE cc_start: 0.7893 (m-80) cc_final: 0.7245 (m-80) REVERT: N 70 THR cc_start: 0.8612 (m) cc_final: 0.8335 (t) REVERT: N 81 GLU cc_start: 0.8825 (tt0) cc_final: 0.8519 (mm-30) REVERT: N 83 ASP cc_start: 0.7982 (m-30) cc_final: 0.7405 (p0) REVERT: N 87 GLN cc_start: 0.8709 (tt0) cc_final: 0.8287 (tt0) REVERT: N 93 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8440 (ttp-110) REVERT: N 94 ASP cc_start: 0.8326 (m-30) cc_final: 0.7902 (m-30) REVERT: O 6 GLN cc_start: 0.7551 (pt0) cc_final: 0.6691 (pt0) REVERT: O 59 TYR cc_start: 0.6178 (m-80) cc_final: 0.5783 (m-80) REVERT: O 82 MET cc_start: 0.6546 (mtp) cc_final: 0.5875 (mmm) REVERT: O 100 MET cc_start: 0.8657 (mtp) cc_final: 0.8191 (mtt) REVERT: O 105 HIS cc_start: 0.7594 (p-80) cc_final: 0.7290 (m-70) REVERT: P 27 GLN cc_start: 0.6966 (mt0) cc_final: 0.6749 (mp10) REVERT: P 51 ILE cc_start: 0.7580 (mm) cc_final: 0.7348 (mm) REVERT: P 71 PHE cc_start: 0.8016 (m-80) cc_final: 0.7592 (m-10) REVERT: P 100 GLN cc_start: 0.7358 (pm20) cc_final: 0.7014 (pm20) REVERT: Q 36 TRP cc_start: 0.8691 (m100) cc_final: 0.7935 (m100) REVERT: Q 93 VAL cc_start: 0.9275 (t) cc_final: 0.9059 (m) REVERT: Q 100 MET cc_start: 0.8336 (mtp) cc_final: 0.7799 (mmt) REVERT: R 27 HIS cc_start: 0.8061 (t-90) cc_final: 0.7613 (t70) REVERT: R 38 GLN cc_start: 0.8106 (tt0) cc_final: 0.7690 (tm-30) REVERT: S 4 LEU cc_start: 0.8281 (mt) cc_final: 0.7909 (mp) REVERT: S 24 VAL cc_start: 0.8303 (t) cc_final: 0.7100 (t) REVERT: S 58 ASN cc_start: 0.7426 (t0) cc_final: 0.7123 (t0) REVERT: S 72 ASP cc_start: 0.7284 (t0) cc_final: 0.7043 (t0) REVERT: S 75 LYS cc_start: 0.8982 (mttt) cc_final: 0.8762 (mtmm) REVERT: S 78 PHE cc_start: 0.5581 (m-80) cc_final: 0.4671 (m-80) REVERT: S 107 THR cc_start: 0.8256 (t) cc_final: 0.7970 (p) outliers start: 2 outliers final: 1 residues processed: 874 average time/residue: 0.3996 time to fit residues: 509.3834 Evaluate side-chains 441 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN A 425 ASN B 577 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 653 GLN D 94 ASN D 203 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN ** F 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 35 GLN O 100 HIS S 100CASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24027 Z= 0.262 Angle : 0.808 11.295 32668 Z= 0.414 Chirality : 0.052 0.381 3946 Planarity : 0.005 0.056 4000 Dihedral : 12.508 83.334 5010 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 12.37 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2780 helix: 0.64 (0.26), residues: 395 sheet: 0.47 (0.16), residues: 897 loop : -0.08 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 338 HIS 0.013 0.002 HIS A 72 PHE 0.039 0.003 PHE O 29 TYR 0.030 0.002 TYR L 49 ARG 0.011 0.001 ARG S 100F *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 567 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8287 (m100) cc_final: 0.7649 (m100) REVERT: A 180 ASP cc_start: 0.8401 (m-30) cc_final: 0.7973 (m-30) REVERT: A 391 PHE cc_start: 0.8746 (m-80) cc_final: 0.8495 (m-10) REVERT: A 426 MET cc_start: 0.6175 (mtp) cc_final: 0.5600 (mtp) REVERT: B 530 MET cc_start: 0.2943 (mmp) cc_final: 0.2457 (mmt) REVERT: B 543 GLN cc_start: 0.6977 (pt0) cc_final: 0.6619 (pt0) REVERT: B 544 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 588 ARG cc_start: 0.8987 (tmm-80) cc_final: 0.8709 (ttm-80) REVERT: B 601 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8289 (mmmt) REVERT: B 628 TRP cc_start: 0.2550 (m-10) cc_final: 0.2309 (m-10) REVERT: C 75 VAL cc_start: 0.8702 (p) cc_final: 0.8393 (m) REVERT: C 95 MET cc_start: 0.8604 (ptp) cc_final: 0.8335 (ptp) REVERT: C 112 TRP cc_start: 0.8104 (m100) cc_final: 0.7619 (m100) REVERT: C 180 ASP cc_start: 0.8875 (m-30) cc_final: 0.8595 (t0) REVERT: C 342 LEU cc_start: 0.9024 (mt) cc_final: 0.8768 (tp) REVERT: C 434 MET cc_start: 0.8939 (ttp) cc_final: 0.8626 (ttp) REVERT: E 557 ARG cc_start: 0.3685 (OUTLIER) cc_final: 0.3349 (mtt-85) REVERT: E 601 LYS cc_start: 0.8374 (mttt) cc_final: 0.7806 (mtmt) REVERT: E 618 SER cc_start: 0.7732 (m) cc_final: 0.7096 (p) REVERT: E 620 ASP cc_start: 0.8746 (p0) cc_final: 0.8385 (p0) REVERT: E 638 TYR cc_start: 0.8192 (m-80) cc_final: 0.7521 (m-80) REVERT: E 639 THR cc_start: 0.8553 (m) cc_final: 0.7933 (p) REVERT: E 644 ASN cc_start: 0.8436 (m-40) cc_final: 0.8108 (m-40) REVERT: E 646 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8372 (mm) REVERT: E 647 GLU cc_start: 0.7483 (pp20) cc_final: 0.7080 (pp20) REVERT: E 648 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 53 PHE cc_start: 0.7775 (m-10) cc_final: 0.7575 (m-80) REVERT: D 80 ASN cc_start: 0.8086 (p0) cc_final: 0.7836 (t0) REVERT: D 116 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8645 (mp) REVERT: D 246 GLN cc_start: 0.6581 (mp10) cc_final: 0.5071 (tp-100) REVERT: D 425 ASN cc_start: 0.8672 (p0) cc_final: 0.8064 (p0) REVERT: D 468 PHE cc_start: 0.7972 (m-80) cc_final: 0.7573 (m-80) REVERT: F 601 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8564 (mmmm) REVERT: F 623 TRP cc_start: 0.8706 (m100) cc_final: 0.8405 (m100) REVERT: H 1 GLN cc_start: 0.7574 (pm20) cc_final: 0.7077 (pp30) REVERT: H 36 TRP cc_start: 0.8502 (m100) cc_final: 0.7694 (m-10) REVERT: H 82 MET cc_start: 0.7052 (tpp) cc_final: 0.6256 (tpp) REVERT: L 4 MET cc_start: 0.6567 (mtm) cc_final: 0.6271 (mtm) REVERT: L 27 GLN cc_start: 0.7351 (tp-100) cc_final: 0.6632 (tm-30) REVERT: L 27 LEU cc_start: 0.7811 (mt) cc_final: 0.7591 (mt) REVERT: L 49 TYR cc_start: 0.7482 (p90) cc_final: 0.7036 (p90) REVERT: L 61 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8011 (mtm-85) REVERT: L 71 PHE cc_start: 0.8639 (m-80) cc_final: 0.8010 (m-80) REVERT: L 79 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7223 (tm-30) REVERT: M 13 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8593 (mmmm) REVERT: M 72 ASP cc_start: 0.7774 (t0) cc_final: 0.7070 (t0) REVERT: M 86 ASP cc_start: 0.8229 (m-30) cc_final: 0.7832 (m-30) REVERT: M 87 THR cc_start: 0.9523 (t) cc_final: 0.9187 (m) REVERT: M 103 TRP cc_start: 0.6915 (m100) cc_final: 0.6374 (m100) REVERT: N 24 ASN cc_start: 0.8262 (t0) cc_final: 0.7759 (t0) REVERT: N 25 ASN cc_start: 0.8249 (m-40) cc_final: 0.7945 (m110) REVERT: N 34 TYR cc_start: 0.7938 (m-80) cc_final: 0.7704 (m-10) REVERT: N 70 THR cc_start: 0.8731 (m) cc_final: 0.8498 (p) REVERT: N 71 LEU cc_start: 0.8468 (tp) cc_final: 0.8220 (tp) REVERT: N 81 GLU cc_start: 0.8526 (tt0) cc_final: 0.8025 (mt-10) REVERT: O 59 TYR cc_start: 0.6223 (m-80) cc_final: 0.5755 (m-80) REVERT: O 75 MET cc_start: 0.8191 (mmm) cc_final: 0.7628 (mtp) REVERT: O 81 LYS cc_start: 0.4687 (OUTLIER) cc_final: 0.4400 (mppt) REVERT: O 82 VAL cc_start: 0.8229 (m) cc_final: 0.7985 (p) REVERT: O 100 MET cc_start: 0.8732 (mtp) cc_final: 0.8383 (mtt) REVERT: P 17 GLN cc_start: 0.8692 (tt0) cc_final: 0.8238 (mm-40) REVERT: P 27 GLN cc_start: 0.6953 (mt0) cc_final: 0.6667 (mp10) REVERT: P 50 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7699 (ptmt) REVERT: P 51 ILE cc_start: 0.8611 (mm) cc_final: 0.8059 (mp) REVERT: P 61 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8321 (mtm110) REVERT: P 71 PHE cc_start: 0.7978 (m-80) cc_final: 0.7353 (m-10) REVERT: P 100 GLN cc_start: 0.7842 (pm20) cc_final: 0.7222 (tm-30) REVERT: Q 36 TRP cc_start: 0.8567 (m100) cc_final: 0.7984 (m100) REVERT: Q 46 GLU cc_start: 0.8205 (tt0) cc_final: 0.7732 (tt0) REVERT: Q 51 ILE cc_start: 0.9358 (tt) cc_final: 0.9149 (tp) REVERT: R 27 HIS cc_start: 0.8318 (t-90) cc_final: 0.7890 (t-170) REVERT: R 38 GLN cc_start: 0.8080 (tt0) cc_final: 0.7787 (tm-30) REVERT: R 42 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7215 (mm-40) REVERT: R 71 PHE cc_start: 0.8047 (m-80) cc_final: 0.7459 (m-80) REVERT: R 90 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: S 24 VAL cc_start: 0.8194 (t) cc_final: 0.7780 (t) REVERT: S 58 ASN cc_start: 0.7584 (t0) cc_final: 0.7226 (t0) REVERT: S 72 ASP cc_start: 0.7429 (t0) cc_final: 0.6951 (t0) REVERT: S 100 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6957 (mm-30) REVERT: S 100 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7550 (p0) REVERT: S 100 VAL cc_start: 0.9390 (t) cc_final: 0.8973 (m) REVERT: T 40 GLN cc_start: 0.7839 (mp10) cc_final: 0.7469 (mm-40) REVERT: T 104 VAL cc_start: 0.9104 (t) cc_final: 0.8809 (m) outliers start: 63 outliers final: 26 residues processed: 594 average time/residue: 0.3651 time to fit residues: 328.3391 Evaluate side-chains 442 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 409 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 374 HIS C 195 ASN C 249 HIS C 425 ASN E 616 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 77 HIS R 27 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 ASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24027 Z= 0.479 Angle : 0.863 12.473 32668 Z= 0.440 Chirality : 0.053 0.404 3946 Planarity : 0.006 0.048 4000 Dihedral : 11.372 82.177 5006 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 4.30 % Allowed : 14.46 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2780 helix: 0.56 (0.27), residues: 400 sheet: 0.05 (0.16), residues: 937 loop : -0.37 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 610 HIS 0.013 0.002 HIS A 72 PHE 0.032 0.003 PHE D 391 TYR 0.051 0.003 TYR E 643 ARG 0.008 0.001 ARG Q 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 424 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8293 (m100) cc_final: 0.7662 (m100) REVERT: A 180 ASP cc_start: 0.8667 (m-30) cc_final: 0.8187 (m-30) REVERT: A 391 PHE cc_start: 0.8963 (m-80) cc_final: 0.8462 (m-80) REVERT: A 426 MET cc_start: 0.6454 (mtp) cc_final: 0.5385 (mtp) REVERT: A 427 TRP cc_start: 0.7308 (m-10) cc_final: 0.6965 (m-90) REVERT: B 577 GLN cc_start: 0.9293 (tp40) cc_final: 0.8898 (tp40) REVERT: B 601 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8325 (mmmm) REVERT: B 628 TRP cc_start: 0.2969 (m-10) cc_final: 0.2658 (m-10) REVERT: C 95 MET cc_start: 0.8620 (ptp) cc_final: 0.8347 (ptp) REVERT: C 103 GLN cc_start: 0.8883 (tp40) cc_final: 0.8160 (tm-30) REVERT: C 165 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8254 (mm) REVERT: C 371 ILE cc_start: 0.8961 (mm) cc_final: 0.8678 (tp) REVERT: C 373 MET cc_start: 0.7801 (mmt) cc_final: 0.7466 (mmm) REVERT: E 601 LYS cc_start: 0.8538 (mttt) cc_final: 0.8079 (pttm) REVERT: E 644 ASN cc_start: 0.8515 (m-40) cc_final: 0.8182 (t0) REVERT: E 647 GLU cc_start: 0.7745 (pp20) cc_final: 0.7212 (pp20) REVERT: E 648 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8386 (mt-10) REVERT: D 246 GLN cc_start: 0.6773 (mp10) cc_final: 0.5250 (tp40) REVERT: D 425 ASN cc_start: 0.8652 (p0) cc_final: 0.8231 (p0) REVERT: D 468 PHE cc_start: 0.8340 (m-80) cc_final: 0.7419 (m-80) REVERT: D 486 TYR cc_start: 0.8999 (m-80) cc_final: 0.8645 (m-10) REVERT: F 542 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7409 (mmt180) REVERT: F 601 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8620 (mmmm) REVERT: F 623 TRP cc_start: 0.9048 (m100) cc_final: 0.8277 (m100) REVERT: F 663 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7481 (tp) REVERT: H 1 GLN cc_start: 0.7626 (pm20) cc_final: 0.7333 (pp30) REVERT: H 33 TYR cc_start: 0.7098 (m-10) cc_final: 0.6865 (m-10) REVERT: H 82 MET cc_start: 0.7481 (tpp) cc_final: 0.6853 (tpp) REVERT: L 4 MET cc_start: 0.7293 (mtm) cc_final: 0.6754 (mtm) REVERT: L 27 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7118 (tm-30) REVERT: L 27 LEU cc_start: 0.8496 (mt) cc_final: 0.7726 (mt) REVERT: L 42 GLN cc_start: 0.8624 (mp10) cc_final: 0.7802 (mp10) REVERT: L 49 TYR cc_start: 0.7864 (p90) cc_final: 0.7460 (p90) REVERT: M 13 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8693 (mmmm) REVERT: M 59 TYR cc_start: 0.8370 (m-80) cc_final: 0.8058 (m-80) REVERT: M 72 ASP cc_start: 0.7959 (t0) cc_final: 0.7269 (t0) REVERT: M 86 ASP cc_start: 0.7979 (m-30) cc_final: 0.7517 (m-30) REVERT: M 103 TRP cc_start: 0.7142 (m100) cc_final: 0.6660 (m100) REVERT: N 24 ASN cc_start: 0.8283 (t0) cc_final: 0.7813 (t0) REVERT: N 36 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7442 (tm-30) REVERT: N 50 SER cc_start: 0.8768 (p) cc_final: 0.8368 (t) REVERT: N 64 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7410 (ttpt) REVERT: N 70 THR cc_start: 0.8796 (m) cc_final: 0.8578 (p) REVERT: N 81 GLU cc_start: 0.8377 (tt0) cc_final: 0.7867 (mm-30) REVERT: N 90 ASP cc_start: 0.8825 (t0) cc_final: 0.8599 (t0) REVERT: O 59 TYR cc_start: 0.6297 (m-80) cc_final: 0.6045 (m-10) REVERT: O 81 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.4961 (mppt) REVERT: O 100 MET cc_start: 0.8449 (mtp) cc_final: 0.8203 (mtt) REVERT: P 4 MET cc_start: 0.6275 (tpt) cc_final: 0.5800 (tpt) REVERT: P 17 GLN cc_start: 0.8704 (tt0) cc_final: 0.8412 (mm-40) REVERT: P 27 GLN cc_start: 0.7140 (mt0) cc_final: 0.6706 (mp10) REVERT: P 49 TYR cc_start: 0.8100 (p90) cc_final: 0.7457 (p90) REVERT: P 50 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7928 (ptmt) REVERT: P 51 ILE cc_start: 0.8674 (mm) cc_final: 0.8110 (mp) REVERT: P 53 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7581 (t0) REVERT: P 71 PHE cc_start: 0.8021 (m-80) cc_final: 0.7779 (m-80) REVERT: P 100 GLN cc_start: 0.7911 (pm20) cc_final: 0.7665 (pm20) REVERT: Q 38 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6798 (ptp-170) REVERT: Q 46 GLU cc_start: 0.8175 (tt0) cc_final: 0.7747 (tt0) REVERT: R 27 HIS cc_start: 0.8388 (t-90) cc_final: 0.7779 (t-170) REVERT: R 39 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6568 (mpp80) REVERT: R 51 ILE cc_start: 0.8590 (mp) cc_final: 0.8243 (mm) REVERT: R 71 PHE cc_start: 0.8243 (m-80) cc_final: 0.7514 (m-80) REVERT: R 94 PHE cc_start: 0.6359 (m-80) cc_final: 0.6153 (m-80) REVERT: S 37 ILE cc_start: 0.7948 (mt) cc_final: 0.7710 (mm) REVERT: S 58 ASN cc_start: 0.7962 (t0) cc_final: 0.7433 (t0) REVERT: S 72 ASP cc_start: 0.7192 (t0) cc_final: 0.6636 (t0) REVERT: T 2 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8463 (mm-30) REVERT: T 18 ARG cc_start: 0.6840 (mmm160) cc_final: 0.6543 (mmm160) REVERT: T 40 GLN cc_start: 0.7549 (mp10) cc_final: 0.7315 (mp10) REVERT: T 48 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.5836 (m-80) outliers start: 107 outliers final: 70 residues processed: 490 average time/residue: 0.3522 time to fit residues: 265.3566 Evaluate side-chains 458 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 381 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 30 ASN S 1 GLN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24027 Z= 0.254 Angle : 0.710 10.708 32668 Z= 0.357 Chirality : 0.049 0.340 3946 Planarity : 0.005 0.042 4000 Dihedral : 10.129 73.736 5006 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 3.86 % Allowed : 16.43 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2780 helix: 0.73 (0.27), residues: 393 sheet: -0.06 (0.16), residues: 921 loop : -0.38 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 69 HIS 0.010 0.001 HIS A 72 PHE 0.028 0.002 PHE T 60 TYR 0.026 0.002 TYR E 643 ARG 0.006 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 423 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8023 (m100) cc_final: 0.7812 (m100) REVERT: A 180 ASP cc_start: 0.8606 (m-30) cc_final: 0.8082 (m-30) REVERT: A 338 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.6543 (p-90) REVERT: A 342 LEU cc_start: 0.8974 (mt) cc_final: 0.8657 (mt) REVERT: A 391 PHE cc_start: 0.8896 (m-80) cc_final: 0.8363 (m-10) REVERT: A 426 MET cc_start: 0.6564 (mtp) cc_final: 0.6279 (mtp) REVERT: B 530 MET cc_start: 0.2942 (mmp) cc_final: 0.2483 (mmm) REVERT: C 103 GLN cc_start: 0.8783 (tp40) cc_final: 0.8125 (tm-30) REVERT: C 165 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 268 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8534 (mmmt) REVERT: C 371 ILE cc_start: 0.8967 (mm) cc_final: 0.8661 (tp) REVERT: E 530 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8489 (tpp) REVERT: E 601 LYS cc_start: 0.8537 (mttt) cc_final: 0.8045 (mtmm) REVERT: E 621 MET cc_start: 0.8461 (ppp) cc_final: 0.8198 (ppp) REVERT: E 644 ASN cc_start: 0.8587 (m-40) cc_final: 0.8359 (t0) REVERT: D 425 ASN cc_start: 0.8607 (p0) cc_final: 0.8171 (p0) REVERT: D 468 PHE cc_start: 0.8115 (m-80) cc_final: 0.7287 (m-80) REVERT: D 486 TYR cc_start: 0.8850 (m-80) cc_final: 0.8488 (m-10) REVERT: F 601 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8645 (mmmm) REVERT: F 623 TRP cc_start: 0.8983 (m100) cc_final: 0.8512 (m100) REVERT: H 82 MET cc_start: 0.7478 (tpp) cc_final: 0.6827 (tpp) REVERT: H 100 MET cc_start: 0.7839 (tpp) cc_final: 0.7271 (tpp) REVERT: L 4 MET cc_start: 0.7285 (mtm) cc_final: 0.6774 (mtm) REVERT: L 27 GLN cc_start: 0.7553 (tp-100) cc_final: 0.7252 (tm-30) REVERT: L 27 LEU cc_start: 0.8338 (mt) cc_final: 0.7470 (mt) REVERT: L 42 GLN cc_start: 0.8634 (mp10) cc_final: 0.7914 (mp10) REVERT: L 49 TYR cc_start: 0.7952 (p90) cc_final: 0.7430 (p90) REVERT: M 72 ASP cc_start: 0.7841 (t0) cc_final: 0.7058 (t0) REVERT: M 86 ASP cc_start: 0.7983 (m-30) cc_final: 0.7513 (m-30) REVERT: M 91 TYR cc_start: 0.8304 (m-80) cc_final: 0.7575 (m-10) REVERT: N 24 ASN cc_start: 0.8323 (t0) cc_final: 0.7853 (t0) REVERT: N 34 TYR cc_start: 0.8025 (m-80) cc_final: 0.7616 (m-10) REVERT: N 36 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7373 (tm-30) REVERT: N 50 SER cc_start: 0.8708 (p) cc_final: 0.8454 (t) REVERT: N 70 THR cc_start: 0.8751 (m) cc_final: 0.8511 (p) REVERT: N 87 GLN cc_start: 0.8134 (tt0) cc_final: 0.7770 (tt0) REVERT: N 90 ASP cc_start: 0.8962 (t0) cc_final: 0.8252 (t0) REVERT: O 59 TYR cc_start: 0.6288 (m-80) cc_final: 0.6086 (m-10) REVERT: P 4 MET cc_start: 0.6378 (tpt) cc_final: 0.5938 (tpt) REVERT: P 17 GLN cc_start: 0.8716 (tt0) cc_final: 0.8397 (mm-40) REVERT: P 27 GLN cc_start: 0.7051 (mt0) cc_final: 0.6683 (mp10) REVERT: P 42 GLN cc_start: 0.8672 (mm110) cc_final: 0.7975 (tp40) REVERT: P 49 TYR cc_start: 0.8190 (p90) cc_final: 0.7926 (p90) REVERT: P 50 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8104 (ttpp) REVERT: P 51 ILE cc_start: 0.8753 (mm) cc_final: 0.8552 (mp) REVERT: P 61 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8365 (mtm110) REVERT: P 87 TYR cc_start: 0.6143 (m-80) cc_final: 0.5502 (m-80) REVERT: P 100 GLN cc_start: 0.7742 (pm20) cc_final: 0.6643 (tm-30) REVERT: Q 12 LEU cc_start: 0.8677 (tp) cc_final: 0.8416 (tp) REVERT: Q 36 TRP cc_start: 0.8670 (m100) cc_final: 0.7693 (m100) REVERT: Q 38 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7329 (ptp-170) REVERT: Q 46 GLU cc_start: 0.8228 (tt0) cc_final: 0.7822 (tt0) REVERT: Q 100 MET cc_start: 0.7828 (mmt) cc_final: 0.7033 (mmp) REVERT: R 27 HIS cc_start: 0.8432 (t-90) cc_final: 0.7866 (t-170) REVERT: R 39 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6554 (mpp80) REVERT: R 51 ILE cc_start: 0.8659 (mp) cc_final: 0.8444 (mm) REVERT: R 94 PHE cc_start: 0.6053 (m-80) cc_final: 0.5831 (m-80) REVERT: S 72 ASP cc_start: 0.7195 (t0) cc_final: 0.6667 (t0) REVERT: S 75 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8602 (mtmm) REVERT: T 2 GLU cc_start: 0.8734 (mm-30) cc_final: 0.7889 (pp20) REVERT: T 18 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6919 (mmm160) REVERT: T 19 ILE cc_start: 0.8992 (mp) cc_final: 0.8747 (mp) REVERT: T 40 GLN cc_start: 0.7528 (mp10) cc_final: 0.7269 (mp10) REVERT: T 48 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.5594 (m-80) outliers start: 96 outliers final: 55 residues processed: 484 average time/residue: 0.3579 time to fit residues: 265.4007 Evaluate side-chains 446 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 385 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN P 53 ASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24027 Z= 0.299 Angle : 0.725 16.127 32668 Z= 0.360 Chirality : 0.049 0.360 3946 Planarity : 0.005 0.057 4000 Dihedral : 9.624 69.419 5006 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.96 % Rotamer: Outliers : 4.10 % Allowed : 16.51 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2780 helix: 0.82 (0.28), residues: 381 sheet: -0.16 (0.16), residues: 944 loop : -0.46 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 47 HIS 0.013 0.002 HIS A 72 PHE 0.030 0.002 PHE P 71 TYR 0.022 0.002 TYR Q 102 ARG 0.009 0.001 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 393 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9255 (ppp) cc_final: 0.8677 (ppp) REVERT: A 112 TRP cc_start: 0.8117 (m100) cc_final: 0.7880 (m100) REVERT: A 180 ASP cc_start: 0.8627 (m-30) cc_final: 0.8165 (m-30) REVERT: A 207 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8864 (ptpp) REVERT: A 338 TRP cc_start: 0.7009 (OUTLIER) cc_final: 0.6457 (p-90) REVERT: B 530 MET cc_start: 0.3186 (mmp) cc_final: 0.2845 (mmm) REVERT: B 621 MET cc_start: 0.8411 (ptm) cc_final: 0.8004 (ppp) REVERT: C 103 GLN cc_start: 0.8824 (tp40) cc_final: 0.8195 (tm-30) REVERT: C 165 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8198 (mm) REVERT: C 371 ILE cc_start: 0.8987 (mm) cc_final: 0.8677 (tp) REVERT: E 530 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8476 (tpp) REVERT: E 601 LYS cc_start: 0.8551 (mttt) cc_final: 0.8070 (mtmm) REVERT: E 621 MET cc_start: 0.8495 (ppp) cc_final: 0.8178 (ppp) REVERT: E 631 TRP cc_start: 0.8812 (t-100) cc_final: 0.8534 (t-100) REVERT: D 425 ASN cc_start: 0.8622 (p0) cc_final: 0.8196 (p0) REVERT: D 468 PHE cc_start: 0.8009 (m-80) cc_final: 0.7195 (m-80) REVERT: D 486 TYR cc_start: 0.8887 (m-80) cc_final: 0.8527 (m-10) REVERT: F 601 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8684 (mmmm) REVERT: F 623 TRP cc_start: 0.9087 (m100) cc_final: 0.8770 (m100) REVERT: F 663 LEU cc_start: 0.8001 (tp) cc_final: 0.7607 (tp) REVERT: H 82 MET cc_start: 0.7526 (tpp) cc_final: 0.6830 (tpp) REVERT: H 100 MET cc_start: 0.7864 (tpp) cc_final: 0.7522 (tpp) REVERT: L 4 MET cc_start: 0.7441 (mtm) cc_final: 0.6663 (mtm) REVERT: L 27 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7331 (tm-30) REVERT: L 27 LEU cc_start: 0.8260 (mt) cc_final: 0.7465 (mt) REVERT: L 42 GLN cc_start: 0.8722 (mp10) cc_final: 0.7995 (mp10) REVERT: L 49 TYR cc_start: 0.8026 (p90) cc_final: 0.7303 (p90) REVERT: M 13 LYS cc_start: 0.9312 (tppt) cc_final: 0.9083 (tppt) REVERT: M 46 GLU cc_start: 0.8339 (tp30) cc_final: 0.8130 (tp30) REVERT: M 56 ASN cc_start: 0.8718 (t0) cc_final: 0.8500 (t0) REVERT: M 72 ASP cc_start: 0.7857 (t0) cc_final: 0.7146 (t0) REVERT: M 86 ASP cc_start: 0.7955 (m-30) cc_final: 0.7430 (m-30) REVERT: M 91 TYR cc_start: 0.8206 (m-80) cc_final: 0.7428 (m-10) REVERT: N 24 ASN cc_start: 0.8203 (t0) cc_final: 0.7824 (t0) REVERT: N 26 ILE cc_start: 0.7872 (mm) cc_final: 0.7515 (mm) REVERT: N 34 TYR cc_start: 0.7984 (m-80) cc_final: 0.7604 (m-10) REVERT: N 50 SER cc_start: 0.8918 (p) cc_final: 0.8586 (t) REVERT: N 70 THR cc_start: 0.8744 (m) cc_final: 0.8512 (p) REVERT: N 85 TYR cc_start: 0.8457 (m-80) cc_final: 0.8104 (m-80) REVERT: N 87 GLN cc_start: 0.8125 (tt0) cc_final: 0.7799 (tt0) REVERT: N 90 ASP cc_start: 0.8818 (t0) cc_final: 0.8512 (t0) REVERT: O 100 MET cc_start: 0.7655 (mtt) cc_final: 0.7407 (mtp) REVERT: P 17 GLN cc_start: 0.8686 (tt0) cc_final: 0.8384 (mm-40) REVERT: P 27 GLN cc_start: 0.7082 (mt0) cc_final: 0.6684 (mp10) REVERT: P 53 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7414 (t0) REVERT: P 61 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8343 (mtm110) REVERT: P 87 TYR cc_start: 0.6098 (m-80) cc_final: 0.5580 (m-80) REVERT: P 100 GLN cc_start: 0.7666 (pm20) cc_final: 0.6680 (tm-30) REVERT: Q 100 MET cc_start: 0.7835 (mmt) cc_final: 0.7224 (mmp) REVERT: R 4 MET cc_start: 0.6686 (mmm) cc_final: 0.6308 (mmt) REVERT: R 27 HIS cc_start: 0.8546 (t-90) cc_final: 0.7962 (t-170) REVERT: R 39 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6529 (mpp80) REVERT: S 72 ASP cc_start: 0.7180 (t0) cc_final: 0.6914 (t0) REVERT: S 75 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8545 (ttpp) REVERT: T 2 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7939 (pp20) REVERT: T 48 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.5799 (m-80) outliers start: 102 outliers final: 71 residues processed: 460 average time/residue: 0.3456 time to fit residues: 246.2813 Evaluate side-chains 440 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 362 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN E 616 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN T 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24027 Z= 0.198 Angle : 0.674 9.477 32668 Z= 0.333 Chirality : 0.048 0.335 3946 Planarity : 0.004 0.040 4000 Dihedral : 8.885 62.900 5006 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.61 % Allowed : 17.63 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2780 helix: 0.91 (0.28), residues: 381 sheet: -0.10 (0.17), residues: 939 loop : -0.44 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 47 HIS 0.009 0.001 HIS D 374 PHE 0.017 0.002 PHE D 391 TYR 0.018 0.001 TYR Q 102 ARG 0.010 0.000 ARG P 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 400 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9162 (ppp) cc_final: 0.8632 (ppp) REVERT: A 180 ASP cc_start: 0.8623 (m-30) cc_final: 0.8230 (m-30) REVERT: A 338 TRP cc_start: 0.7078 (OUTLIER) cc_final: 0.6336 (p-90) REVERT: B 544 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7475 (tt) REVERT: B 621 MET cc_start: 0.8334 (ptm) cc_final: 0.7567 (ppp) REVERT: C 103 GLN cc_start: 0.8712 (tp40) cc_final: 0.8135 (tm-30) REVERT: C 165 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8131 (mm) REVERT: C 371 ILE cc_start: 0.8987 (mm) cc_final: 0.8660 (tp) REVERT: E 601 LYS cc_start: 0.8490 (mttt) cc_final: 0.8035 (mtmm) REVERT: E 621 MET cc_start: 0.8515 (ppp) cc_final: 0.8179 (ppp) REVERT: E 631 TRP cc_start: 0.8712 (t-100) cc_final: 0.8475 (t-100) REVERT: E 647 GLU cc_start: 0.7693 (pp20) cc_final: 0.7406 (pp20) REVERT: E 648 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 180 ASP cc_start: 0.8486 (m-30) cc_final: 0.7909 (t0) REVERT: D 317 PHE cc_start: 0.8193 (t80) cc_final: 0.7879 (t80) REVERT: D 423 ILE cc_start: 0.9577 (mt) cc_final: 0.8852 (mt) REVERT: D 468 PHE cc_start: 0.7879 (m-80) cc_final: 0.6980 (m-80) REVERT: D 486 TYR cc_start: 0.8669 (m-80) cc_final: 0.8365 (m-10) REVERT: F 601 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8616 (mmmm) REVERT: F 621 MET cc_start: 0.8507 (tpp) cc_final: 0.8305 (tpp) REVERT: F 623 TRP cc_start: 0.9073 (m100) cc_final: 0.8736 (m100) REVERT: F 663 LEU cc_start: 0.8034 (tp) cc_final: 0.7673 (tp) REVERT: H 25 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: H 82 MET cc_start: 0.7483 (tpp) cc_final: 0.6920 (tpp) REVERT: H 102 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6003 (t80) REVERT: L 4 MET cc_start: 0.7657 (mtm) cc_final: 0.7100 (mtm) REVERT: L 27 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7352 (tm-30) REVERT: L 27 LEU cc_start: 0.8212 (mt) cc_final: 0.7680 (mp) REVERT: L 49 TYR cc_start: 0.7996 (p90) cc_final: 0.7307 (p90) REVERT: L 77 ARG cc_start: 0.8835 (mtm110) cc_final: 0.8544 (ptp-170) REVERT: M 13 LYS cc_start: 0.9336 (tppt) cc_final: 0.9116 (tppt) REVERT: M 46 GLU cc_start: 0.8254 (tp30) cc_final: 0.7884 (tp30) REVERT: M 56 ASN cc_start: 0.8705 (t0) cc_final: 0.8487 (t0) REVERT: M 58 ASN cc_start: 0.7546 (t0) cc_final: 0.7202 (t0) REVERT: M 72 ASP cc_start: 0.7847 (t0) cc_final: 0.7130 (t0) REVERT: M 86 ASP cc_start: 0.8008 (m-30) cc_final: 0.7527 (m-30) REVERT: M 91 TYR cc_start: 0.8156 (m-80) cc_final: 0.7365 (m-10) REVERT: N 24 ASN cc_start: 0.8387 (t0) cc_final: 0.7939 (t0) REVERT: N 25 ASN cc_start: 0.8208 (m-40) cc_final: 0.7969 (m-40) REVERT: N 34 TYR cc_start: 0.7993 (m-80) cc_final: 0.7587 (m-10) REVERT: N 36 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7223 (tm-30) REVERT: N 50 SER cc_start: 0.8822 (p) cc_final: 0.8477 (t) REVERT: N 64 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7853 (tttt) REVERT: N 85 TYR cc_start: 0.8455 (m-80) cc_final: 0.8123 (m-80) REVERT: N 90 ASP cc_start: 0.8845 (t0) cc_final: 0.8594 (t0) REVERT: P 17 GLN cc_start: 0.8647 (tt0) cc_final: 0.8428 (mm-40) REVERT: P 27 GLN cc_start: 0.7053 (mt0) cc_final: 0.6672 (mp10) REVERT: P 61 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8349 (mtm110) REVERT: P 87 TYR cc_start: 0.6021 (m-80) cc_final: 0.5488 (m-80) REVERT: P 100 GLN cc_start: 0.7476 (pm20) cc_final: 0.6626 (tm-30) REVERT: Q 36 TRP cc_start: 0.8647 (m100) cc_final: 0.7648 (m100) REVERT: Q 100 MET cc_start: 0.7737 (mmt) cc_final: 0.7236 (mmp) REVERT: R 27 HIS cc_start: 0.8535 (t-90) cc_final: 0.7989 (t-170) REVERT: R 39 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6680 (mpp80) REVERT: R 71 PHE cc_start: 0.8429 (m-80) cc_final: 0.8219 (m-10) REVERT: R 85 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7132 (tt) REVERT: S 72 ASP cc_start: 0.7024 (t0) cc_final: 0.6714 (t0) REVERT: S 75 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8488 (ttpp) REVERT: T 2 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8048 (pp20) REVERT: T 48 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.5845 (m-80) outliers start: 90 outliers final: 55 residues processed: 449 average time/residue: 0.3439 time to fit residues: 240.9830 Evaluate side-chains 437 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 373 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 87 GLN Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24027 Z= 0.185 Angle : 0.666 9.539 32668 Z= 0.328 Chirality : 0.048 0.333 3946 Planarity : 0.004 0.040 4000 Dihedral : 8.486 59.576 5006 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 3.05 % Allowed : 18.59 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2780 helix: 0.80 (0.28), residues: 389 sheet: -0.03 (0.17), residues: 938 loop : -0.46 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M 47 HIS 0.009 0.001 HIS D 374 PHE 0.017 0.002 PHE S 53 TYR 0.019 0.001 TYR Q 102 ARG 0.008 0.000 ARG T 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 397 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9152 (ppp) cc_final: 0.8587 (ppp) REVERT: A 104 MET cc_start: 0.8686 (tpp) cc_final: 0.8427 (tpp) REVERT: A 125 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9162 (tp) REVERT: A 180 ASP cc_start: 0.8585 (m-30) cc_final: 0.8185 (m-30) REVERT: A 338 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6108 (p-90) REVERT: A 361 PHE cc_start: 0.7733 (m-80) cc_final: 0.7040 (m-80) REVERT: B 530 MET cc_start: 0.3220 (mmt) cc_final: 0.3020 (mmt) REVERT: B 577 GLN cc_start: 0.9338 (tp40) cc_final: 0.9120 (mm-40) REVERT: B 621 MET cc_start: 0.8320 (ptm) cc_final: 0.7593 (ppp) REVERT: C 103 GLN cc_start: 0.8638 (tp40) cc_final: 0.8089 (tm-30) REVERT: C 165 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8108 (mm) REVERT: C 317 PHE cc_start: 0.9112 (t80) cc_final: 0.8758 (t80) REVERT: C 371 ILE cc_start: 0.8955 (mm) cc_final: 0.8631 (tp) REVERT: E 530 MET cc_start: 0.8454 (tpp) cc_final: 0.8110 (mmm) REVERT: E 601 LYS cc_start: 0.8411 (mttt) cc_final: 0.8058 (mtmm) REVERT: E 621 MET cc_start: 0.8523 (ppp) cc_final: 0.8164 (ppp) REVERT: E 647 GLU cc_start: 0.7673 (pp20) cc_final: 0.7382 (pp20) REVERT: E 648 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8106 (mt-10) REVERT: D 180 ASP cc_start: 0.8432 (m-30) cc_final: 0.8211 (t0) REVERT: D 317 PHE cc_start: 0.8221 (t80) cc_final: 0.7931 (t80) REVERT: D 468 PHE cc_start: 0.7940 (m-80) cc_final: 0.7016 (m-80) REVERT: D 486 TYR cc_start: 0.8649 (m-80) cc_final: 0.8356 (m-10) REVERT: F 601 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8616 (mmmm) REVERT: F 623 TRP cc_start: 0.8987 (m100) cc_final: 0.8488 (m100) REVERT: F 663 LEU cc_start: 0.8081 (tp) cc_final: 0.7752 (tp) REVERT: H 25 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: H 46 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: H 82 MET cc_start: 0.7507 (tpp) cc_final: 0.6943 (tpp) REVERT: H 102 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.6082 (t80) REVERT: L 4 MET cc_start: 0.7523 (mtm) cc_final: 0.6736 (mtm) REVERT: L 9 LEU cc_start: 0.9053 (mt) cc_final: 0.8571 (tp) REVERT: L 27 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7407 (tm-30) REVERT: L 27 LEU cc_start: 0.8404 (mt) cc_final: 0.7690 (mt) REVERT: L 49 TYR cc_start: 0.7844 (p90) cc_final: 0.7626 (p90) REVERT: L 77 ARG cc_start: 0.8779 (mtm110) cc_final: 0.8459 (ptp-170) REVERT: M 13 LYS cc_start: 0.9377 (tppt) cc_final: 0.9172 (tppt) REVERT: M 46 GLU cc_start: 0.8053 (tp30) cc_final: 0.7607 (tp30) REVERT: M 56 ASN cc_start: 0.8966 (t0) cc_final: 0.8649 (t0) REVERT: M 58 ASN cc_start: 0.7847 (t0) cc_final: 0.7509 (t0) REVERT: M 72 ASP cc_start: 0.7659 (t0) cc_final: 0.6950 (t0) REVERT: M 86 ASP cc_start: 0.7968 (m-30) cc_final: 0.7467 (m-30) REVERT: M 91 TYR cc_start: 0.8185 (m-80) cc_final: 0.7376 (m-10) REVERT: N 24 ASN cc_start: 0.8386 (t0) cc_final: 0.8023 (p0) REVERT: N 34 TYR cc_start: 0.7947 (m-80) cc_final: 0.7583 (m-10) REVERT: N 36 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7329 (tm-30) REVERT: N 50 SER cc_start: 0.8775 (p) cc_final: 0.8424 (t) REVERT: N 85 TYR cc_start: 0.8519 (m-80) cc_final: 0.8177 (m-80) REVERT: N 87 GLN cc_start: 0.8000 (tt0) cc_final: 0.7737 (tt0) REVERT: N 90 ASP cc_start: 0.8894 (t0) cc_final: 0.8693 (t0) REVERT: O 100 MET cc_start: 0.7882 (mtp) cc_final: 0.7581 (mtp) REVERT: P 17 GLN cc_start: 0.8625 (tt0) cc_final: 0.8405 (mm-40) REVERT: P 27 GLN cc_start: 0.7028 (mt0) cc_final: 0.6571 (mp10) REVERT: P 61 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8133 (ptp90) REVERT: P 87 TYR cc_start: 0.5970 (m-80) cc_final: 0.5494 (m-80) REVERT: P 100 GLN cc_start: 0.7503 (pm20) cc_final: 0.6653 (tm-30) REVERT: Q 57 THR cc_start: 0.9191 (p) cc_final: 0.8980 (t) REVERT: Q 100 MET cc_start: 0.7672 (mmt) cc_final: 0.7222 (mmp) REVERT: R 27 HIS cc_start: 0.8507 (t-90) cc_final: 0.7957 (t-170) REVERT: R 39 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6703 (mpp80) REVERT: R 71 PHE cc_start: 0.8408 (m-80) cc_final: 0.8152 (m-10) REVERT: S 72 ASP cc_start: 0.7000 (t0) cc_final: 0.6682 (t0) REVERT: S 75 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8436 (ttpp) REVERT: T 2 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8124 (pp20) REVERT: T 48 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.5846 (m-80) outliers start: 76 outliers final: 53 residues processed: 437 average time/residue: 0.3495 time to fit residues: 238.7978 Evaluate side-chains 432 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 371 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 80 optimal weight: 0.0070 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 182 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24027 Z= 0.208 Angle : 0.665 14.494 32668 Z= 0.326 Chirality : 0.048 0.340 3946 Planarity : 0.004 0.045 4000 Dihedral : 8.125 59.077 5006 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 3.45 % Allowed : 18.84 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2780 helix: 0.79 (0.28), residues: 395 sheet: 0.00 (0.16), residues: 952 loop : -0.47 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 47 HIS 0.008 0.001 HIS D 374 PHE 0.019 0.002 PHE S 53 TYR 0.017 0.001 TYR Q 102 ARG 0.014 0.001 ARG T 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 385 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9197 (ppp) cc_final: 0.8634 (ppp) REVERT: A 180 ASP cc_start: 0.8574 (m-30) cc_final: 0.8184 (m-30) REVERT: A 338 TRP cc_start: 0.7131 (OUTLIER) cc_final: 0.6030 (p-90) REVERT: A 361 PHE cc_start: 0.7717 (m-80) cc_final: 0.7077 (m-80) REVERT: B 635 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7532 (mm) REVERT: C 103 GLN cc_start: 0.8651 (tp40) cc_final: 0.8118 (tm-30) REVERT: C 165 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 317 PHE cc_start: 0.9091 (t80) cc_final: 0.8732 (t80) REVERT: C 371 ILE cc_start: 0.8928 (mm) cc_final: 0.8616 (tp) REVERT: E 530 MET cc_start: 0.8440 (tpp) cc_final: 0.8038 (mmt) REVERT: E 601 LYS cc_start: 0.8400 (mttt) cc_final: 0.8050 (mtmm) REVERT: E 621 MET cc_start: 0.8431 (ppp) cc_final: 0.8086 (ppp) REVERT: E 647 GLU cc_start: 0.7695 (pp20) cc_final: 0.7407 (pp20) REVERT: E 648 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 84 VAL cc_start: 0.8650 (t) cc_final: 0.8339 (m) REVERT: D 317 PHE cc_start: 0.8330 (t80) cc_final: 0.8053 (t80) REVERT: D 468 PHE cc_start: 0.7947 (m-80) cc_final: 0.7013 (m-80) REVERT: D 486 TYR cc_start: 0.8655 (m-80) cc_final: 0.8394 (m-10) REVERT: F 621 MET cc_start: 0.8224 (tpp) cc_final: 0.7979 (tpp) REVERT: F 623 TRP cc_start: 0.9112 (m100) cc_final: 0.8565 (m100) REVERT: H 25 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7698 (m-10) REVERT: H 46 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: H 82 MET cc_start: 0.7539 (tpp) cc_final: 0.6955 (tpp) REVERT: H 102 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6255 (t80) REVERT: L 4 MET cc_start: 0.7548 (mtm) cc_final: 0.6798 (mtm) REVERT: L 9 LEU cc_start: 0.9005 (mt) cc_final: 0.8551 (tp) REVERT: L 27 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7402 (tm-30) REVERT: L 27 LEU cc_start: 0.8396 (mt) cc_final: 0.7626 (mt) REVERT: L 49 TYR cc_start: 0.7793 (p90) cc_final: 0.7531 (p90) REVERT: L 77 ARG cc_start: 0.8761 (mtm110) cc_final: 0.8471 (ptt-90) REVERT: M 13 LYS cc_start: 0.9384 (tppt) cc_final: 0.9177 (tppt) REVERT: M 56 ASN cc_start: 0.8996 (t0) cc_final: 0.8718 (t0) REVERT: M 58 ASN cc_start: 0.7840 (t0) cc_final: 0.7484 (t0) REVERT: M 72 ASP cc_start: 0.7673 (t0) cc_final: 0.6981 (t0) REVERT: M 86 ASP cc_start: 0.7974 (m-30) cc_final: 0.7480 (m-30) REVERT: M 91 TYR cc_start: 0.8175 (m-80) cc_final: 0.7234 (m-10) REVERT: N 24 ASN cc_start: 0.8382 (t0) cc_final: 0.8011 (p0) REVERT: N 34 TYR cc_start: 0.7928 (m-80) cc_final: 0.7588 (m-10) REVERT: N 50 SER cc_start: 0.8737 (p) cc_final: 0.8391 (t) REVERT: N 87 GLN cc_start: 0.7946 (tt0) cc_final: 0.7217 (tp40) REVERT: N 90 ASP cc_start: 0.8838 (t0) cc_final: 0.8557 (t0) REVERT: O 100 MET cc_start: 0.7975 (mtp) cc_final: 0.7697 (mtp) REVERT: P 17 GLN cc_start: 0.8637 (tt0) cc_final: 0.8417 (mm-40) REVERT: P 42 GLN cc_start: 0.8785 (mm110) cc_final: 0.8146 (tm-30) REVERT: P 61 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8039 (ptp90) REVERT: P 87 TYR cc_start: 0.5852 (m-80) cc_final: 0.5477 (m-80) REVERT: P 100 GLN cc_start: 0.7406 (pm20) cc_final: 0.6623 (tm-30) REVERT: Q 43 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7838 (mtmm) REVERT: Q 100 MET cc_start: 0.7607 (mmt) cc_final: 0.7176 (mmp) REVERT: R 1 ASP cc_start: 0.7705 (m-30) cc_final: 0.7182 (t0) REVERT: R 27 HIS cc_start: 0.8507 (t-90) cc_final: 0.7967 (t-170) REVERT: R 39 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6647 (mpp80) REVERT: R 71 PHE cc_start: 0.8374 (m-80) cc_final: 0.8087 (m-10) REVERT: S 72 ASP cc_start: 0.7046 (t0) cc_final: 0.6724 (t0) REVERT: S 75 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8463 (ttpp) REVERT: T 2 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8129 (pp20) REVERT: T 48 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.5950 (m-80) outliers start: 86 outliers final: 60 residues processed: 438 average time/residue: 0.3225 time to fit residues: 221.0796 Evaluate side-chains 435 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 367 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 82 MET Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 225 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24027 Z= 0.232 Angle : 0.684 12.810 32668 Z= 0.334 Chirality : 0.048 0.357 3946 Planarity : 0.004 0.048 4000 Dihedral : 7.799 59.531 5006 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 3.21 % Allowed : 19.44 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2780 helix: 0.78 (0.29), residues: 389 sheet: 0.05 (0.17), residues: 915 loop : -0.55 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 47 HIS 0.013 0.001 HIS A 72 PHE 0.024 0.002 PHE A 159 TYR 0.015 0.001 TYR Q 102 ARG 0.008 0.000 ARG T 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 382 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9245 (ppp) cc_final: 0.8990 (ppp) REVERT: A 180 ASP cc_start: 0.8607 (m-30) cc_final: 0.8225 (m-30) REVERT: A 338 TRP cc_start: 0.7033 (OUTLIER) cc_final: 0.5651 (p-90) REVERT: A 361 PHE cc_start: 0.7666 (m-80) cc_final: 0.6970 (m-80) REVERT: C 103 GLN cc_start: 0.8615 (tp40) cc_final: 0.8175 (tm-30) REVERT: C 165 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8238 (mm) REVERT: C 317 PHE cc_start: 0.9115 (t80) cc_final: 0.8718 (t80) REVERT: C 371 ILE cc_start: 0.8943 (mm) cc_final: 0.8626 (tp) REVERT: E 530 MET cc_start: 0.8490 (tpp) cc_final: 0.8118 (mmt) REVERT: E 551 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6618 (tm-30) REVERT: E 601 LYS cc_start: 0.8448 (mttt) cc_final: 0.8072 (mtmm) REVERT: E 621 MET cc_start: 0.8444 (ppp) cc_final: 0.8100 (ppp) REVERT: E 647 GLU cc_start: 0.7713 (pp20) cc_final: 0.7396 (pp20) REVERT: E 648 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8156 (mt-10) REVERT: D 84 VAL cc_start: 0.8666 (t) cc_final: 0.8342 (m) REVERT: D 468 PHE cc_start: 0.7899 (m-80) cc_final: 0.7041 (m-80) REVERT: D 486 TYR cc_start: 0.8730 (m-80) cc_final: 0.8515 (m-10) REVERT: F 534 SER cc_start: 0.9161 (m) cc_final: 0.8561 (p) REVERT: F 621 MET cc_start: 0.8355 (tpp) cc_final: 0.7973 (tpp) REVERT: F 623 TRP cc_start: 0.9158 (m100) cc_final: 0.8774 (m100) REVERT: F 663 LEU cc_start: 0.7681 (tp) cc_final: 0.7278 (tp) REVERT: H 25 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: H 46 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: H 82 MET cc_start: 0.7541 (tpp) cc_final: 0.6950 (tpp) REVERT: H 102 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6295 (t80) REVERT: L 4 MET cc_start: 0.7545 (mtm) cc_final: 0.6701 (mtm) REVERT: L 9 LEU cc_start: 0.9021 (mt) cc_final: 0.8562 (tp) REVERT: L 27 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7476 (tm-30) REVERT: L 27 LEU cc_start: 0.8276 (mt) cc_final: 0.7617 (mt) REVERT: L 42 GLN cc_start: 0.8671 (mp10) cc_final: 0.7928 (mp10) REVERT: L 49 TYR cc_start: 0.7822 (p90) cc_final: 0.7529 (p90) REVERT: L 77 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8127 (ptp90) REVERT: M 13 LYS cc_start: 0.9397 (tppt) cc_final: 0.9190 (tppt) REVERT: M 56 ASN cc_start: 0.9064 (t0) cc_final: 0.8822 (t0) REVERT: M 58 ASN cc_start: 0.7957 (t0) cc_final: 0.7585 (t0) REVERT: M 72 ASP cc_start: 0.7697 (t0) cc_final: 0.7133 (t0) REVERT: M 77 GLU cc_start: 0.8852 (pp20) cc_final: 0.8203 (pp20) REVERT: M 86 ASP cc_start: 0.7935 (m-30) cc_final: 0.7425 (m-30) REVERT: N 24 ASN cc_start: 0.8359 (t0) cc_final: 0.7955 (p0) REVERT: N 34 TYR cc_start: 0.7968 (m-80) cc_final: 0.7624 (m-10) REVERT: N 50 SER cc_start: 0.8744 (p) cc_final: 0.8411 (t) REVERT: N 87 GLN cc_start: 0.7940 (tt0) cc_final: 0.7419 (tp40) REVERT: O 100 MET cc_start: 0.7900 (mtp) cc_final: 0.7600 (mtp) REVERT: P 4 MET cc_start: 0.6319 (tpt) cc_final: 0.5677 (tpt) REVERT: P 17 GLN cc_start: 0.8638 (tt0) cc_final: 0.8402 (mm-40) REVERT: P 61 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8080 (ptp90) REVERT: P 68 GLU cc_start: 0.8810 (mm-30) cc_final: 0.7664 (tp30) REVERT: P 87 TYR cc_start: 0.5856 (m-80) cc_final: 0.5571 (m-80) REVERT: Q 43 LYS cc_start: 0.8230 (mtmm) cc_final: 0.8018 (mtmm) REVERT: Q 100 MET cc_start: 0.7608 (mmt) cc_final: 0.7193 (mmp) REVERT: R 1 ASP cc_start: 0.7799 (m-30) cc_final: 0.7340 (t0) REVERT: R 27 HIS cc_start: 0.8499 (t-90) cc_final: 0.8034 (t-170) REVERT: R 39 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6656 (mpp80) REVERT: R 71 PHE cc_start: 0.8301 (m-80) cc_final: 0.8054 (m-10) REVERT: S 72 ASP cc_start: 0.7013 (t0) cc_final: 0.6682 (t0) REVERT: S 75 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8508 (ttpp) REVERT: T 2 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8146 (pp20) REVERT: T 48 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.5942 (m-80) outliers start: 80 outliers final: 63 residues processed: 429 average time/residue: 0.3407 time to fit residues: 228.3762 Evaluate side-chains 436 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 366 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** P 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN T 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24027 Z= 0.223 Angle : 0.678 12.221 32668 Z= 0.333 Chirality : 0.048 0.358 3946 Planarity : 0.004 0.048 4000 Dihedral : 7.679 58.910 5006 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 3.25 % Allowed : 19.60 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2780 helix: 0.74 (0.28), residues: 390 sheet: -0.01 (0.17), residues: 935 loop : -0.57 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP M 47 HIS 0.008 0.001 HIS D 374 PHE 0.032 0.002 PHE A 159 TYR 0.017 0.001 TYR Q 102 ARG 0.008 0.000 ARG T 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 375 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9246 (ppp) cc_final: 0.8645 (ppp) REVERT: A 107 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: A 180 ASP cc_start: 0.8643 (m-30) cc_final: 0.8132 (m-30) REVERT: A 338 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.5501 (p-90) REVERT: A 361 PHE cc_start: 0.7741 (m-80) cc_final: 0.7066 (m-80) REVERT: A 427 TRP cc_start: 0.7441 (m-10) cc_final: 0.7146 (m-90) REVERT: B 621 MET cc_start: 0.8022 (ppp) cc_final: 0.7783 (ppp) REVERT: C 103 GLN cc_start: 0.8606 (tp40) cc_final: 0.8095 (tm-30) REVERT: C 317 PHE cc_start: 0.9094 (t80) cc_final: 0.8715 (t80) REVERT: C 371 ILE cc_start: 0.8965 (mm) cc_final: 0.8646 (tp) REVERT: E 530 MET cc_start: 0.8488 (tpp) cc_final: 0.8116 (mmt) REVERT: E 551 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6669 (tm-30) REVERT: E 601 LYS cc_start: 0.8435 (mttt) cc_final: 0.8100 (mtmm) REVERT: E 621 MET cc_start: 0.8443 (ppp) cc_final: 0.8101 (ppp) REVERT: E 647 GLU cc_start: 0.7824 (pp20) cc_final: 0.7523 (pp20) REVERT: E 648 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 84 VAL cc_start: 0.8719 (t) cc_final: 0.8395 (m) REVERT: D 468 PHE cc_start: 0.7926 (m-80) cc_final: 0.7074 (m-80) REVERT: F 528 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7570 (p) REVERT: F 534 SER cc_start: 0.9066 (m) cc_final: 0.8440 (p) REVERT: F 621 MET cc_start: 0.8346 (tpp) cc_final: 0.7996 (tpp) REVERT: F 623 TRP cc_start: 0.9167 (m100) cc_final: 0.8854 (m100) REVERT: F 663 LEU cc_start: 0.7682 (tp) cc_final: 0.7315 (tp) REVERT: H 25 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: H 46 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: H 102 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6354 (t80) REVERT: H 108 ARG cc_start: 0.7498 (tmt-80) cc_final: 0.7292 (tmt-80) REVERT: L 4 MET cc_start: 0.7646 (mtm) cc_final: 0.7373 (mtm) REVERT: L 9 LEU cc_start: 0.9064 (mt) cc_final: 0.8620 (tp) REVERT: L 27 LEU cc_start: 0.8218 (mt) cc_final: 0.7662 (mt) REVERT: L 42 GLN cc_start: 0.8638 (mp10) cc_final: 0.7900 (mp10) REVERT: M 13 LYS cc_start: 0.9403 (tppt) cc_final: 0.9189 (tppt) REVERT: M 56 ASN cc_start: 0.9047 (t0) cc_final: 0.8811 (t0) REVERT: M 58 ASN cc_start: 0.8039 (t0) cc_final: 0.7641 (t0) REVERT: M 72 ASP cc_start: 0.7580 (t0) cc_final: 0.6906 (t0) REVERT: M 86 ASP cc_start: 0.8008 (m-30) cc_final: 0.7536 (m-30) REVERT: M 91 TYR cc_start: 0.8420 (m-10) cc_final: 0.7831 (m-10) REVERT: N 24 ASN cc_start: 0.8361 (t0) cc_final: 0.7959 (p0) REVERT: N 34 TYR cc_start: 0.7937 (m-80) cc_final: 0.7609 (m-10) REVERT: N 50 SER cc_start: 0.8770 (p) cc_final: 0.8428 (t) REVERT: N 87 GLN cc_start: 0.7671 (tt0) cc_final: 0.7263 (tp40) REVERT: O 59 TYR cc_start: 0.6835 (m-10) cc_final: 0.6599 (m-10) REVERT: O 69 MET cc_start: 0.7048 (mtt) cc_final: 0.6585 (mtt) REVERT: O 100 MET cc_start: 0.8054 (mtp) cc_final: 0.7421 (mtm) REVERT: P 17 GLN cc_start: 0.8638 (tt0) cc_final: 0.8400 (mm-40) REVERT: P 61 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8071 (ptp90) REVERT: P 68 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7375 (tp30) REVERT: P 87 TYR cc_start: 0.5856 (m-80) cc_final: 0.5541 (m-80) REVERT: Q 100 MET cc_start: 0.7586 (mmt) cc_final: 0.7195 (mmp) REVERT: R 1 ASP cc_start: 0.7815 (m-30) cc_final: 0.7367 (t70) REVERT: R 27 HIS cc_start: 0.8504 (t-90) cc_final: 0.8066 (t-170) REVERT: R 39 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6683 (mpp80) REVERT: S 72 ASP cc_start: 0.7213 (t0) cc_final: 0.6881 (t0) REVERT: S 75 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8495 (ttpp) REVERT: S 105 GLN cc_start: 0.8182 (mp10) cc_final: 0.7961 (tp40) REVERT: T 2 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8187 (pp20) REVERT: T 48 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6118 (m-80) outliers start: 81 outliers final: 65 residues processed: 425 average time/residue: 0.3297 time to fit residues: 219.9433 Evaluate side-chains 435 residues out of total 2490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 362 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 32 HIS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 39 ARG Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 653 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN T 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082367 restraints weight = 67984.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081958 restraints weight = 46368.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082845 restraints weight = 37970.048| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24027 Z= 0.247 Angle : 0.695 12.649 32668 Z= 0.339 Chirality : 0.048 0.381 3946 Planarity : 0.004 0.048 4000 Dihedral : 7.635 58.302 5006 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 3.13 % Allowed : 20.28 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2780 helix: 0.70 (0.28), residues: 390 sheet: -0.01 (0.17), residues: 919 loop : -0.59 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP M 47 HIS 0.008 0.001 HIS D 374 PHE 0.024 0.002 PHE A 159 TYR 0.029 0.001 TYR L 49 ARG 0.008 0.000 ARG T 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5241.72 seconds wall clock time: 95 minutes 34.56 seconds (5734.56 seconds total)